In hydrodesulfurization (HDS) of fossil fuels, the sulfur levels are reduced by sulfur extraction from hydrocarbons through a series of catalyzed reaction steps on low-coordinated sites on molybdenum disulfide (MoS(2)) nanoclusters. By means of scanning tunneling microscopy (STM), we show that the adsorption properties of MoS(2) nanoclusters toward the HDS refractory dibenzothiophene (DBT) vary dramatically with small changes in the cluster size. STM images reveal that MoS(2) nanoclusters with a size above a threshold value of 1.5 nm react with hydrogen to form so-called sulfur vacancies predominately located at edge sites, but these edge vacancies are not capable of binding DBT directly. In contrast, MoS(2) nanoclusters below the threshold perform remarkably better. Here, sulfur vacancies form predominantly at the corner sites, and these vacancies show a high affinity for DBT. The results thus indicate that very small MoS(2) nanoclusters may have unique catalytic properties for the production of clean fuels.